The Firefly Effect
by maria100
Summary: New Story. Chapter 1 uploaded. When Sheppard develops some mysterious powers the Atlantis team is faced with a difficult choice: To save the city or to save their Colonel... Warnings for Sheppard whump.
1. Chapter 1

**A/N – Hey guys. Here's my new story. I hope you enjoy it. The usual disclaimers apply, insert witty Sheppard gag here! I don't own Stargate and am making no money from this story. This is a rewrite of a story I posted 5 years ago. I'd appreciate reviews and any con-crit if you have the time. Big thanks to my betas Athena's Owl and Venea Taur for their invaluable help and support. They made this story so much better through their advice. Also big thanks to my sister and muse EloraSheppard for being my sounding board and all out expert on everything Stargate and physics related. **

**Stargate Atlantis - The Firefly Effect**

**Set – Season Three – Shortly after Tao of Rodney**

**Spoilers – The Return, most previous episodes**

**Main Characters – This is a Atlantis whole team fic, which focuses lots on Atlantis as there weren't enough episodes that explored that amazing city. Most characters are involved but Sheppard has the starring role.**

**~SGA~**

**The Firefly Effect**

**Chapter One**

**By Maria100**

Lt. Colonel John Sheppard was contemplating murder. Cold blooded, knife through the heart murder. His hands gripped the Puddle Jumper controls tightly as the ship sped through the Stargate, leaving the control room behind them. He tried to tune out the cause of his murderous thoughts as he gazed intently into the blackness of space.

"I mean seriously, how you ever got your pilots licence is beyond me," McKay's voice grumbled on. "I don't know why I'm trusting you again, especially after your recent antics. How we didn't crash into the city, I don't know."

Sheppard clenched his teeth together tightly. McKay had started this particular rant shortly after arriving in the Jumper Bay ten minutes before and hadn't let up since. Sheppard had long since stopped answering the scientist's complaints but McKay had resolutely continued his tirade.

"Doctor McKay, were you not told by Doctor Weir that you could stay behind for this mission and look into the computer malfunctions? Besides, you know full well that Colonel Sheppard's flying has saved many lives, including your own. He would not put us in harm's way needlessly," said Teyla.

Sheppard snorted; Teyla was ever the diplomat. He angled the ancient controls down, ignoring McKay's intake of breath as the Jumper began its descent. Below them the planet began to loom larger and landmasses became visible. Sheppard had always known that there was something special about flying. Back on Earth, he had thought that no moment would beat the first time he had flown an Apache helicopter but then he came to Atlantis and discovered Puddle Jumpers.

"Watch it, flyboy, there's nothing chasing us this time." McKay's grip tightened on the edges of the chair.

Sheppard sighed heavily and called up the HUD. "Focus McKay. Do you see anything worth checking out?"

McKay hesitantly let go of the chair and picked up his data pad. His fingers tapped rapidly across the screen before he looked up. "I'm picking up some strange energy readings from the northern hemisphere."

Sheppard looked carefully at the HUD, which, at his thought, zoomed in on the northern part of the planet. It showed him a large continent that was easily the size of Asia. "Any way you could narrow that down slightly, McKay?"

McKay huffed irritably. "I'm trying, it's just-" McKay swivelled in his chair to face Ronon, who was absently fiddling with his gun. "That is not helping me concentrate. Go play with your gun somewhere else, Conan."

"Where exactly do you want me to go? We're on a spaceship," said Ronon, purposefully flicking the gun from stun to kill.

"Oh, I'm sure I could think of somewhere."

Sheppard took a deep breath and eased the jumper into a low orbit. "McKay, the energy readings..."

"If you want me to work quicker, you need to keep him under control. Besides, I've already located them." McKay quickly turned back to the HUD. "They're coming from here." He leant over to tap the image, pointing to an area towards the middle of the landmass. Sheppard quickly keyed in the co-ordinates and the jumper slowly began its controlled dive, breaking through the atmosphere and giving the team their first clear glimpse of the land below.

"Anyone want to bet on what we'll find down there?" Sheppard turned to face his team, gently releasing the controls.

"Eyes forward, Sheppard. You're no Starbuck!"

"Cool it, McKay, it's all under control." Sheppard turned back to the view of the rapidly approaching ground. He barely managed to stifle a smirk as he heard a small whimper from the seat beside him. Finally, after deciding that torturing McKay was maybe not worth the effort of explaining another crashed Jumper to Elizabeth, he pulled the controls back. The jumper slowed and gently began to land.

The muted thump of the jumper touching ground was swiftly followed by a hefty sigh from McKay as he tentatively let go of the chair and stretched out his fingers. Sheppard stood up and clipped his P90 back to his TAC vest. Ronon and Teyla were already up and opening the rear hatch. "You ready?" he asked, turning to Rodney.

'Yes, yes," McKay said, stumbling to his feet. Sheppard gave his jumper one last affectionate pat before joining Ronon and Teyla. The sun hit his face as soon as he left the jumper and he squinted slightly, pulling his sunglasses from his top pocket. He quickly surveyed the immediate area, scanning the wide-open expanse in front of them.

"Oh that's just great," Rodney said, coming to stand beside Sheppard. "I didn't put any sun-cream on, and you know how easily I burn."

Sheppard gritted his teeth, mentally counting to ten. He closed the rear hatch and pocketed the remote. "Rodney, why don't you look and see where the energy readings are coming from? The quicker we start..." Sheppard trailed off, noting the surrounding forest in the distance and worn grass that seemed to become a crude, dirt pathway up ahead. "Okay. Let's go. Rodney, you lead. Ronon, you take our six."

"Wait, why do I have to lead?" said McKay. Sheppard looked pointedly at the data pad in the scientist's hands. Flustered, McKay hastily checked the screen, "Alright, we need to head that way." McKay headed off towards the tree line without a backwards glance. Sheppard looked to Ronon and Teyla, sharing the sufferance that often accompanied missions with McKay, before grudgingly following.

"Just say the word, Sheppard," said Ronon. Sheppard heard the soft whir of Ronon's energy pistol powering up.

"Don't tempt me," he muttered quietly.

The team walked slowly along the dusty trail. Sheppard appreciated the gentle breeze cooling his face as he travelled in the hot sun; the layers of his uniform were not ideal for comfort with temperatures as high as these. Sheppard thought longingly of sea breezes and cool waves. In his opinion, surfing was the only activity to be done on sweltering summer days.

As they approached the dense woodland, Sheppard heard the soft trill of a songbird and the rustle of the leaves. He followed McKay into the shade of the trees and sighed gratefully as the temperature plunged, pocketing his sunglasses. The forest was packed with vegetation, making it hard to see further than a few meters ahead. The path they were following became narrow and winding before it seemed to be swallowed by shadow. A short, sharp scream cut through the forest, disturbing the peace that had reigned just moments before. Sheppard jerked up a fist. Ronon and Teyla froze beside him. Sheppard hurriedly checked on his errant scientist who was still lumbering around ahead. Again, he held up a fist but received a bewildered stare from McKay.

Sheppard shook his head and decisively lifted his P90, flicking off the safety. "Hold on for a minute, would you?" He nodded to Ronon who, without speaking, seemingly melted into the surroundings.

McKay groaned, "You're not going to investigate are you? Come on, it's got nothing to do with us. Let the locals murder each other without our help for once. The power source is this way."

Sheppard pointedly stepped past him and slowly inched deeper into the forest. He stayed on the path, heading towards the disturbance. He turned to direct his team to follow but frowned as McKay stumbled, tripping on overgrown roots that were impeding the walkway. Teyla nimbly stepped over the hazard and smiled reassuringly at McKay. Again, Sheppard heard the high-pitched scream; this time followed by frenzied laughter. In front of him, the dirt path ended and the tree line thinned. Slowly, he crouched down, signalling to his team behind him to do the same. He carefully took in the small clearing that could be seen, now that they were clear of the trees. Sunlight filtered through the surrounding forest, causing Sheppard to hastily replace his sunglasses. The field was no more than ten paces across and Sheppard could see the forest continued on, dark and shadowy, on the other side of the clearing. The field was covered in long, wild grass and Sheppard could smell something sweet. It almost reminded him of lavender. McKay sneezed rowdily behind him. As Sheppard watched he saw three small children run out from behind a tree, one boy chasing two girls, giggles spilling from them. They couldn't be more than seven; their movements still betraying some of the awkwardness of the young. Sheppard lowered his gun. He crouched motionless, watching the children. The children were caught up in their game, the boy tugging the smaller girl's blond plaits and pulling her down into a messy heap. The other girl squeaked and jumped out of the reach of his arms. She stared at him as he stepped closer, before grinning and raising her arms.

The boy stamped his foot. "No cheating! Dia you promised."

Sheppard grinned at his team-mates. "Wait here, I don't think we're in too much danger." He received a nod from Teyla but McKay scowled, tapping his fingers restlessly on the data pad. With a roll of his eyes, Sheppard eased himself up leisurely, not wanting to scare the young children and then walked out into the bright sunlight. The sudden movement caused the young girl with blond-braided hair to look his way, her eyes round at the sudden interruption to their game. She hastily scrambled to her feet, shuffling closer to her friends. The boy spun round to face them, grabbing tight hold of the smaller girl's hand. All three children edged backwards, their gaze fixed on Sheppard.

Sheppard raised his hands carefully and gave his most goofy smile as all three children continued to stare. "Hey kids. We're kinda lost. Any chance you could-" Before he could finish the children spun around and scattered, heading towards the trees on the other side of the small clearing. "Teyla a little help here."

Teyla stepped forward, holding her arms out to the fleeing children. "We mean you no harm. We are just travellers looking to trade." As she spoke, the smaller girl tripped. She fell to the ground with a muffled squeak. The boy stopped short in his headlong run, frozen on the edge of the clearing. Teyla cautiously moved towards the fallen child. The girl was clutching her leg, eyes squeezed shut, and her long skirts were tangled around her tiny body.

Sheppard looked round for the other child. The clearing was small and he couldn't see any sign of the older girl. He needed to calm the situation before it got any worse. Glancing over at the boy, Sheppard saw that he seemed ready to bolt, but was staring wide-eyed towards the young girl. Sheppard thought through his options. He could just grab the boy; Sheppard's longer strides would get him the short distance to the boy before he could get far. However, scaring small kids wasn't really high up on Sheppard's favourite things to do. The boy was still watching the scene unfolding in the middle of the clearing, fists clenched.

Teyla gently knelt down beside the girl, wiping the tears from the girl's cheeks and brushing back the blond strands that were sticking to the girl's forehead. "My name is Teyla. We just want to help you. Where are you hurt?" The girl whimpered slightly and grabbed the Athosian's hand, her smaller fingers encircling Teyla's tightly. The young boy stared fixedly at the pair in the overgrown grass but seemed unable or unwilling to move towards his fallen playmate.

"Easy kid, easy," Sheppard said, again holding up his hands, in what he hoped was the universal sign of peace. "We just want to help." Sheppard walked over to join Teyla, ushering the boy over to join him. The boy stood immobile, ignoring Sheppard, until another squeal from the girl wrenched him forward and he crept over. His eyes darted to McKay who was busily drumming his fingers over the pad and shaking his head. Sheppard glared at McKay before smiling back at the boy. "Don't mind him kid, now why don't you tell me your name?"

The small boy looked up at Sheppard. "I am Pado." The boy's voice was barely more than a whisper and his gaze kept darting around the clearing.

"Nice to meet you Pado. My name is John, that's Teyla," Teyla smiled and bobbed her head. "And over there is McKay."

McKay put his hands on his hips. "Is this going to take long? I would just like to point out that the energy readings are moving away. I don't know how much longer I can track them for."

"Knock it off McKay." Sheppard turned back to Teyla, who was gently stroking the girl's hair. The girl's eyes were still closed and another small whimper escaped her lips. "Now Pado, can you tell me your friends name?"

"That is Charu." Pado bit his lip and took a tentative step forward, glancing over at McKay apprehensively who was still pacing around the small clearing.

"Rodney!" Sheppard snapped.

McKay stomped over and sat down on a tree stump, pouring over his data pad. "Fine just ignore me. I'll just go over these readings until the energy readings disappear."

Sheppard saw the tension in Pado's little frame ease slightly. The boy looked to Sheppard. "Will she be alright?"

Sheppard smiled. "I hope so, why don't you go hold her hand. It might make her calmer."

Pado scrambled over and seized the girl's hand. "Charu, Charu, you alright? Open your eyes."

Charu opened her eyes, sobbing quietly. Sheppard knelt down beside her. "Hey Charu. My name's John. Where're you hurt?"

Charu took a faltering breath. "My ankle-"

"Okay, Charu, now I'm just gonna have a quick look. I'll be gentle." Sheppard carefully lifted her foot and winced at her sudden intake of breath. Sheppard took in the injury, the blood slowly seeping through her skirts, the glisten of white. He looked at Teyla steadily. "Compound fracture," he muttered. He looked down at the shivers that were wracking the tiny figure. "Right, Pado. Why don't you talk to me about your village? You too, Charu."

Sheppard began rummaging around in his pockets, finding the sterile bandage in his top vest pocket. "So you live with mom and dad?" he prompted. Pado was staring at the stain spreading across Charu's clothes. "Pado. Look at me." Sheppard urged. "I'm going to help her but I need you to talk."

Pado nodded and stiffened his shoulders. "We live in the village by the city ruins. Charu lives with her grandfather. He is the town mayor, isn't he Ru?" He squeezed her hand and she looked up at him, taking a deep breath.

"Grandpa will be cross. I got dirty again." She let go of Teyla and gripped onto the boy, clinging tightly with both hands.

"I will tell him what happened. He won't blame you."

Sheppard picked up a long stick from the ground and lent back over the girl. "This might hurt a little bit. Can you be brave?" Charu nodded, knuckles whitening as her grip tightened on Pado's arm.

Sheppard pushed up the girl's skirts, angling his body over the injury, blocking it from inquisitive eyes. He placed the gauze over the open wound, comforted to see the flow of blood sluggishly turning into a trickle. He looked over his panting patient before laying the stick along her leg, as close to the injury as he dared. The groans from the girl made him pause, even though he had steeled himself against them. "Almost there..." He wrapped the bandage snug around the make-shift splint, holding the leg tight as the girl began to frantically twist her body away. "Done. It's done." The bandage secure he looked over at the children and Teyla.

Teyla lifted the girl's head onto her lap. "Charu, you were very brave. I believe your grandfather would be very proud of you."

Wiping the sweat from his brow, Sheppard pushed himself to his feet. "Pado we need to get Charu back to your village. Can you lead the way?"

Pado nodded quickly, pulling his hands away from Charu. He hurried to his feet. "It is this way," he said, pointing towards the dirt path Sheppard had taken into the forest.

Sheppard stooped, gently lifting Charu into his arms. "Rodney, you ready? Ronon, no need to skulk anymore. We're headed out." Sheppard looked over the bundle in his arms waiting for the runner to emerge.

Ronon lightly jumped down from his vantage point. "Did you see the other girl, Sheppard?"

"No, she must have run off. Pado, will she be alright?"

Pado smiled, his eyes lighting up for the first time, "You mean Dia? She's fine. By now, she will already be back in the village."

McKay's eyes brightened. "She walked back already? So this village is close? I could really do with a rest." Sheppard quirked his eyebrows, glancing at the stump that McKay had just risen from.

Pado frowned, confused. "It is quite far. Dia doesn't need to walk-" he stopped suddenly, suspicion clear in his eyes.

Teyla looked to the sun that was still visible in the gaps between the trees above. "Sundown is approaching Colonel. We should hurry, before these children are missed."

Sheppard shifted Charu carefully and frowned down at Pado, "How could she not have to walk? Don't tell me she can fly? Never mind." He added, on receiving a puzzled look from the boy. "Lead the way."

Pado bounded off down the winding pathway, back into the gloom of the forest. McKay stuffed the data pad into his backpack, trudging after the boy. Sheppard followed, carrying Charu, whose eyes were once again tightly shut. As he moved further into the thicket, he listened carefully. The forest was silent. A jarring hush had settled over the surroundings. Sheppard, itching to feel the strength and comfort of his P90, turned, frowning at Ronon and Teyla, before turning to catch up with McKay and Pado.

"So, tell me a little more about these ruins by your village." Sheppard matched his stride to that of the shorter boy's.

"What would you like to know?" Pado asked, reaching out to hold onto the bottom of Sheppard's TAC vest.

Sheppard felt the small tug and smiled down at the boy. "You know, is it a good place to play? What's there? Was the city destroyed by the Wraith?"

"What are the Wraith? And we aren't allowed to go there. Elder Nethin says it's too dangerous." Again Sheppard felt the boy's puzzled look pass over him.

"You know the Wraith, big monsters, very scary. They come in ships and take people."

"I don't believe in monsters anymore! I'm not a baby." Pado said, crossing his arms. Sheppard halted and looked back at his team, shrugging and raising his eyebrows.

"Maybe the Wraith don't visit this planet," Ronon suggested.

Teyla shook her head. "But it is most unusual to come across a world that is untouched by the Wraith. It is most intriguing, do you not agree Colonel?"

"Yeah, this world just became a lot more interesting."

McKay snorted. "More interesting! Well if you hadn't been playing nursemaid, we would already be investigating those very interesting energy readings."

"Maybe there is a shield or weapon that keeps the Wraith at bay." Sheppard looked down at Charu as her arms clenched uncomfortably around his neck. "Enough. This is a conversation for later. Keep going Pado."

Silence descended over the group as they carried on. Sheppard stepped carefully, peering around Charu, trying to avoid the weeds and logs that were an ever present tripping hazard. At long last the path opened up and sunlight began to overtake shadow. The sun was low in the sky, blinding Sheppard as he stepped out of the shade. They had barely taken a dozen steps out the forest when Sheppard heard several loud cracks around him and the quiet whir of Ronon's gun powering up.

**~SGA~**

**A/N – Thanks for reading guys. I hope to have the next chapter up within the fortnight. For those of you that read and liked the original, the plot hasn't changed but hopefully it is executed a little better. I'd really love to hear from you even if it's just one word!**


	2. Chapter 2

**A/N – Sorry to disappoint anyone who clicks on this chapter but due to me replacing the content in the old chapters, this was the only way to get Fanfiction to send out the alerts to tell people the chapter had been rewritten.**

**The next chapter will be here within 2 weeks and sorry to for bending the rules slightly.**

**Here's an excerpt from Chapter 2 to tide you over:**

Sheppard glanced over to Ronon who was standing with his arms crossed but an observant eye could see the tension in his large frame. He was currently trying to stare down one of the larger hunters. Sheppard turned back to Folan. "That's just Ronon, once you get to know him, he's like a big, soft puppy."

A high-pitched beeping noise started up suddenly. The hunters hastily raised their guns and Folan roughly pushed Pado behind him. Sheppard heard what sounded like a happy grunt from behind him. _Though, you couldn't really tell with Ronon, _Sheppard thought.

The noise was becoming more insistent and Sheppard listened carefully, trying to pinpoint the source of the sound. "Isn't that coming from your pack, McKay?"

"What? Sorry I was just thinking about a certain blond air force Col-" He coughed hurriedly. "Never mind. What did you say? Oh the beeping!" McKay unclipped his backpack, pulling out his data pad. He soon became engrossed in whatever was showing on the screen.

Sheppard again grinned at the hunters surrounding them who were staring at the device in McKay's hands. "Yeah that's a computer. It does lots of cool stuff like card games and er... tetris."

McKay snorted, looking up from the screen. "Like that will mean anything to these Neanderthals. They probably think we are magicians or something."

"Be nice Rodney, they have guns."

"Yes well guns don't equal advanced civilisations."

Sheppard gritted his teeth, turning his smile into a grimace. "Not really what I meant."


End file.
